This study explores the biosynthesis of pipecolic acid-containing cyclodepsipeptides produced by the fungus Penicillium brasilianum LaBioMMi-136, an endophytic fungus from Melia azedarach. Through genome mining, gene knockout, and in vitro enzymatic assays, we identified a biosynthetic gene cluster responsible for their production and uncovered pipecolic acid's biosynthesis in the fungus. This dataset integrates LC-HRMS and NMR data. Access to the data is restricted for publication reasons. For further information, please contact the responsible authors.